Setup

Load R libraries

library(data.table)
library(ggplot2)
library(ggpubr)
library(tidyr)
library(limma)
library(biomaRt)
library(fgsea)
library(goseq)

theme_set(theme_classic())

cell_type_name = params$cell_type_name
graph_weight = params$graph_weight

cell_type_name
## [1] "Micro-PVM"
graph_weight
## [1] "2.0"

Check enrichment of gene sets

Read in gene info and gene set assignments

file_tag = sprintf("%s_%s", cell_type_name, graph_weight)

assayed_genes = scan(sprintf("output/gene_list_%s.txt", file_tag), 
                     what = character(), sep="\n")

gene_sets = scan(sprintf("output/name_s_%s.txt", file_tag), 
                 what = character(), sep="\n")

gene_sets = sapply(gene_sets, strsplit, split=",")
n_genes   = sapply(gene_sets, length)
names(n_genes) = NULL
summary(n_genes)
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##    35.0    38.0    39.0    39.1    41.0    42.0
length(n_genes)
## [1] 40
sort(n_genes)
##  [1] 35 35 37 37 37 37 37 37 38 38 38 38 38 38 39 39 39 39 39 39 39 39 39 39 39
## [26] 39 40 41 41 41 41 41 41 41 41 41 41 42 42 42

Find gene symbols

Find gene symbols from bioMart.

All the gene symbols that can be found in bioMart are consistent with what we have. So no need to run it.

ensembl = useMart("ensembl", dataset = "hsapiens_gene_ensembl")

gene_BM = getBM(attributes = c("hgnc_symbol", "external_gene_name"), 
                filters = "external_gene_name", 
                values = assayed_genes, 
                mart = ensembl)
length(assayed_genes)
dim(gene_BM)
gene_BM[1:2,]

table(assayed_genes %in% gene_BM$external_gene_name)

t1 = table(gene_BM$external_gene_name)
dup = names(t1)[t1 > 1]
gene_BM[gene_BM$external_gene_name %in% dup,]

table(gene_BM$hgnc_symbol == gene_BM$external_gene_name)
w2kp = which(gene_BM$hgnc_symbol != gene_BM$external_gene_name)
gene_BM[w2kp,]

Find gene symbols using the alias2Symbol function from limma.

a2s = rep(NA, length(assayed_genes))
for(i in 1:length(assayed_genes)){
  gi = assayed_genes[i]
  ai = alias2Symbol(gi)
  if(length(ai) > 1){
    print(gi)
    print(ai)
  }
  a2s[i] = ai[1]
}

table(is.na(a2s))
## 
## FALSE  TRUE 
##  1739   261
table(a2s == assayed_genes, useNA = 'ifany')
## 
## FALSE  TRUE  <NA> 
##    21  1718   261
gene_info = data.table(sym_in_data = assayed_genes, sym_limma = a2s)

gene_info[sym_in_data != sym_limma,]
##     sym_in_data   sym_limma
##  1:       LRRC6     DNAAF11
##  2:    C11orf49      CSTPP1
##  3:   LINC00476 ERCC6L2-AS1
##  4:  HNRNPA1P48   HNRNPA1L3
##  5:  ZRANB2-AS2   ZRANB2-DT
##  6:   LINC00271     AHI1-DT
##  7:    RFX3-AS1     RFX3-DT
##  8:   LINC00884  ATP13A3-DT
##  9:   FBXO30-DT    EPM2A-DT
## 10:   LINC00894    EOLA2-DT
## 11:   COX10-AS1    COX10-DT
## 12:   LINC01184  SLC12A2-DT
## 13: FAM198B-AS1  GASK1B-AS1
## 14:     C5orf17   LINC02899
## 15: C8orf37-AS1 CFAP418-AS1
## 16:   LINC01146       HISLA
## 17:      BTBD11       ABTB3
## 18:       H2BU1      H2BC26
## 19:      SKIV2L       SKIC2
## 20:     FAM155A       NALF1
## 21:  CTB-41I6.2   PIK3R5-DT
##     sym_in_data   sym_limma
gene_info[, gene_symbol := sym_in_data]
gene_info[which(sym_in_data != sym_limma & (gene_symbol != "MT-CO2")), 
                gene_symbol := sym_limma]

dim(gene_info)
## [1] 2000    3
gene_info[1:5,]
##    sym_in_data sym_limma gene_symbol
## 1:        CFTR      CFTR        CFTR
## 2:        ICA1      ICA1        ICA1
## 3:        PDK4      PDK4        PDK4
## 4:       CALCR     CALCR       CALCR
## 5:       ABCB4     ABCB4       ABCB4
t1 = table(gene_info$gene_symbol)
table(t1)
## t1
##    1 
## 2000

Prepare gene set information

Gene set annotations (by gene symbols) were downloaded from MSigDB website.

gmtfile = list()
gmtfile[["reactome"]] = "../Annotation/c2.cp.reactome.v2023.2.Hs.symbols.gmt"
gmtfile[["go_bp"]]    = "../Annotation/c5.go.bp.v2023.2.Hs.symbols.gmt"

pathways = list()
for(k1 in names(gmtfile)){
  pathways[[k1]] = gmtPathways(gmtfile[[k1]])
}

names(pathways)
## [1] "reactome" "go_bp"
sapply(pathways, length)
## reactome    go_bp 
##     1692     7647

Filter gene sets for size between 10 and 500.

lapply(pathways, function(v){
  quantile(sapply(v, length), probs = seq(0, 1, 0.1), na.rm = TRUE)
})
## $reactome
##     0%    10%    20%    30%    40%    50%    60%    70%    80%    90%   100% 
##    5.0    7.0    9.0   12.0   17.0   23.0   31.0   44.0   71.8  120.9 1463.0 
## 
## $go_bp
##     0%    10%    20%    30%    40%    50%    60%    70%    80%    90%   100% 
##    5.0    6.0    8.0   10.0   14.0   19.0   29.0   46.0   80.8  183.0 1966.0
for(k1 in names(pathways)){
  p1 = pathways[[k1]]
  pathways[[k1]] = p1[sapply(p1, length) %in% 10:500]
}

Conduct enrichment analysis

dim(gene_info)
## [1] 2000    3
gene_info[1:2,]
##    sym_in_data sym_limma gene_symbol
## 1:        CFTR      CFTR        CFTR
## 2:        ICA1      ICA1        ICA1
gene_dat = fread(sprintf("data/%s_genes_info.csv", cell_type_name))
dim(gene_dat)
## [1] 36517     9
gene_dat[1:2,]
##           gene_ids feature_is_filtered feature_name feature_reference
## 1: ENSG00000000003               FALSE       TSPAN6    NCBITaxon:9606
## 2: ENSG00000000005               FALSE         TNMD    NCBITaxon:9606
##    feature_biotype n_cells_by_counts mean_counts pct_dropout_by_counts
## 1:            gene                76    0.002350               99.8100
## 2:            gene                 1    0.000025               99.9975
##    total_counts
## 1:           94
## 2:            1
length(unique(gene_info$sym_in_data))
## [1] 2000
table(gene_info$sym_in_data %in% gene_dat$feature_name)
## 
## TRUE 
## 2000
table(gene_dat$feature_name %in% gene_info$sym_in_data)
## 
## FALSE  TRUE 
## 34517  2000
gene_dat$selected = 0
gene_dat$selected[match(gene_info$sym_in_data, gene_dat$feature_name)] = 1

table(gene_dat$selected)
## 
##     0     1 
## 34517  2000
tapply(gene_dat$pct_dropout_by_counts, gene_dat$selected, summary)
## $`0`
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##    0.00   94.48   99.58   93.53   99.97  100.00 
## 
## $`1`
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.6475 65.5944 84.3650 76.3053 93.6756 97.9950
gene_info = merge(gene_info, gene_dat, by.x="sym_in_data", 
                  by.y="feature_name", all.x = TRUE, all.y = FALSE)
dim(gene_info)
## [1] 2000   12
gene_info[1:2,]
##    sym_in_data sym_limma gene_symbol        gene_ids feature_is_filtered
## 1:        AATK      AATK        AATK ENSG00000181409               FALSE
## 2:        ABAT      ABAT        ABAT ENSG00000183044               FALSE
##    feature_reference feature_biotype n_cells_by_counts mean_counts
## 1:    NCBITaxon:9606            gene              3157    0.091525
## 2:    NCBITaxon:9606            gene              9074    0.368950
##    pct_dropout_by_counts total_counts selected
## 1:               92.1075         3661        1
## 2:               77.3150        14758        1
max_n2kp = 10

goseq_res = NULL

for(k in 1:length(gene_sets)){
  if(length(gene_sets[[k]]) < 10) { next }
  
  print(k)
  set_k = paste0("set_", k)
  print(gene_sets[[k]])
  
  genes = gene_info$sym_in_data %in% gene_sets[[k]]
  names(genes) = gene_info$gene_symbol
  table(genes)
  
  pwf = nullp(genes, "hg38", "geneSymbol", 
              bias.data = 100 - gene_info$pct_dropout_by_counts)
  
  for(k1 in names(pathways)){
    p1 = pathways[[k1]]
    res1 = goseq(pwf, "hg38", "geneSymbol", 
                 gene2cat=goseq:::reversemapping(p1))
    res1$FDR  = p.adjust(res1$over_represented_pvalue, method="BH")
    
    nD = sum(res1$FDR < 0.05)
    
    if(nD > 0){
      res1 = res1[order(res1$FDR),][1:min(nD, max_n2kp),]
      res1$category = gsub("REACTOME_|GOBP_", "", res1$category)
      res1$category = gsub("_", " ", res1$category)
      res1$category = tolower(res1$category)
      res1$category = substr(res1$category, start=1, stop=81)
      goseq_res[[set_k]][[k1]] = res1
    }
  }
}
## [1] 1
##  [1] "CEACAM1"       "HAMP"          "DUOX1"         "RAB40B"       
##  [5] "FOLR2"         "ADGRG2"        "FLJ40194"      "DLEU7"        
##  [9] "FAM177B"       "HNRNPA1P48"    "EDNRB-AS1"     "LINC01375"    
## [13] "ENTPD1-AS1"    "SLC8A1-AS1"    "RP11-142M10.2" "SRGAP2-AS1"   
## [17] "AC092431.3"    "RNASEH2B-AS1"  "RP11-353M9.1"  "RP11-666F17.1"
## [21] "RP11-796E2.4"  "FAM198B-AS1"   "RP11-360F5.1"  "AC006160.5"   
## [25] "RP11-281P23.2" "RP11-238K6.1"  "RP11-649G15.2" "RP11-452H21.1"
## [29] "RP11-513G19.1" "RP11-486A14.2" "RP11-136F16.1" "RP11-370I10.2"
## [33] "RP11-517O13.1" "ABHD15-AS1"    "RP11-264E23.4" "RP11-7F3.1"   
## [37] "AC009166.9"    "RP11-56I23.2"  "EME2"

## [1] 2
##  [1] "OSBPL6"   "P3H2"     "GCNT2"    "TENT5A"   "RALGPS2"  "NRN1"    
##  [7] "MIS18BP1" "KCNMB1"   "AIG1"     "SLC25A25" "MAGI1"    "PTPN14"  
## [13] "KCNMA1"   "TIAM1"    "TMEM169"  "PLEKHA7"  "NXN"      "S100Z"   
## [19] "MBOAT1"   "SH3RF3"   "NCKAP5"   "APOO"     "PLEKHA5"  "RASSF2"  
## [25] "MICU1"    "DENND1A"  "SLC35E1"  "ZBTB46"   "STARD13"  "DENND4C" 
## [31] "SLC12A6"  "SRSF12"   "AGAP1"    "SLC43A2"  "FAM110B"  "TANC2"   
## [37] "SIPA1L1"

## [1] 3
##  [1] "ABCB4"          "ARL5C"          "AZIN2"          "RASGEF1C"      
##  [5] "TMEM163"        "GHRL"           "GASK1B"         "ADAMTS15"      
##  [9] "MICOS10"        "MARCHF3"        "PLCXD3"         "KBTBD12"       
## [13] "AC007879.5"     "RP1-30E17.2"    "CCDC26"         "AC002539.1"    
## [17] "LINC02642"      "COX10-AS1"      "LINC01141"      "KCNMB2-AS1"    
## [21] "LINC02008"      "RP11-246A10.1"  "XACT"           "LINC02057"     
## [25] "LINC01091"      "AC008697.1"     "LINC01094"      "RP11-745L13.2" 
## [29] "CTC-575N7.1"    "MAILR"          "SMIM35"         "RP11-554D14.6" 
## [33] "LINC02444"      "RP11-588H23.3"  "RP11-72M17.1"   "RP11-399K21.11"
## [37] "LINC02712"      "LINC01374"      "RP11-692P14.1"  "RP11-321P16.3" 
## [41] "RP1-236J16.3"

## [1] 4
##  [1] "BEX1"         "ENPP3"        "SLC9B1"       "GPR85"        "TCERG1L"     
##  [6] "WEE2-AS1"     "AC011288.2"   "COA6-AS1"     "LINC00996"    "ZNF528-AS1"  
## [11] "TENM1"        "FGF14"        "ATP8A2"       "STXBP5L"      "TENM2"       
## [16] "CNTN5"        "ADGRL3"       "ZNF385D"      "SPOCK1"       "AK5"         
## [21] "NCAM2"        "CAMK2N1"      "GABRB1"       "CSMD3"        "LRFN5"       
## [26] "NEGR1"        "FUT9"         "KCTD16"       "FLRT2"        "LSAMP"       
## [31] "PTPRT"        "TAFA2"        "LINC00632"    "FAM155A"      "MEG3"        
## [36] "RP11-191L9.4" "AC093843.1"   "SHISA9"       "RP11-384F7.2" "AGBL1"       
## [41] "IQCJ-SCHIP1"

## [1] 5
##  [1] "RBL1"         "PRTFDC1"      "DAAM1"        "ARHGEF18"     "ARSB"        
##  [6] "LRRC6"        "ZSCAN5A"      "MTHFS"        "RALGPS1"      "MAMDC2"      
## [11] "ARHGAP42"     "CDYL2"        "LCLAT1"       "SCAI"         "LINC00476"   
## [16] "C5orf64"      "FIGN"         "KIAA0825"     "CENPP"        "SCOC-AS1"    
## [21] "RANBP17"      "ATP6AP1L"     "LIN52"        "SLC16A1-AS1"  "RP11-120D5.1"
## [26] "RORA-AS1"     "LINC00506"    "SNX25"        "E2F3"         "GABRG2"      
## [31] "HELLS"        "NR6A1"        "GREM1"        "FRMD3"        "CDH4"        
## [36] "SERTAD2"      "SYCP2"        "RP5-864K19.4" "CYP1B1-AS1"   "HCG17"       
## [41] "C2orf27A"

## [1] 6
##  [1] "CELSR3"               "ZNF365"               "RBMS3"               
##  [4] "CLSTN2"               "NRG2"                 "PRICKLE2"            
##  [7] "ARHGEF3"              "RANBP3L"              "ADGRV1"              
## [10] "FSTL5"                "HPSE2"                "LRRC3B"              
## [13] "POTEG"                "CACNA1E"              "ZNF521"              
## [16] "LINC00970"            "XKR9"                 "AC023469.1"          
## [19] "ROR1-AS1"             "SATB1-AS1"            "LINC01435"           
## [22] "RP11-147G16.1"        "RP11-154D17.1"        "AC013463.2"          
## [25] "AC002066.1"           "CTC-340A15.2"         "USP2-AS1"            
## [28] "RP11-696N14.1"        "RP1-179N16.6"         "LINC01609"           
## [31] "RP11-661A12.5"        "RMST"                 "RP11-20D14.3"        
## [34] "RP11-396B14.2"        "MTRNR2L12"            "RMRP_ENSG00000269900"
## [37] "LINC00551"            "CH507-513H4.1"        "CH507-528H12.1"      
## [40] "RP11-596C23.6"        "RP4-799O8.1"          "RP11-398J12.1"

## [1] 7
##  [1] "SYNDIG1"       "PLAT"          "FAM149A"       "TMEM156"      
##  [5] "ARMH4"         "RP11-493L12.4" "ARHGAP6"       "FSTL4"        
##  [9] "DDX3Y"         "PILRA"         "TGFB2"         "GRK3"         
## [13] "ITGB8"         "SERPINE1"      "BICRAL"        "PADI2"        
## [17] "OGFRL1"        "CDH26"         "TIAM2"         "SLC2A13"      
## [21] "DHRS13"        "NCMAP"         "GLDN"          "CCDC73"       
## [25] "NHEJ1"         "ZNF846"        "CYRIA"         "ZDBF2"        
## [29] "GCC2-AS1"      "AC025171.1"    "LNCAROD"       "MYO16-AS1"    
## [33] "FMN1"          "RP11-351A11.1" "RP11-111A21.1" "RP11-707P17.1"
## [37] "RP11-358F13.1" "RP11-404C6.6"  "RP11-452F19.4"

## [1] 8
##  [1] "SIGLEC1"       "PCSK1N"        "MAP3K8"        "FLVCR2"       
##  [5] "F13A1"         "ENOSF1"        "IFI44L"        "CH25H"        
##  [9] "HERC6"         "UBE2Q2"        "FHAD1"         "TMEM44"       
## [13] "ADAMTS19"      "ADGRA3"        "BEX3"          "MT1E"         
## [17] "OLR1"          "ODF3B"         "H2BC4"         "MX2"          
## [21] "H2BC18"        "TMSB4X"        "MS4A4E"        "RP11-123B3.2" 
## [25] "RP5-1101C3.1"  "ARHGAP8"       "LINC01258"     "LINC02196"    
## [29] "ZNF10"         "RP1-71H24.1"   "OVCH1-AS1"     "RP11-323I15.5"
## [33] "LINC01572"     "RP11-386I14.4" "H2BC8"         "H2AC8"        
## [37] "RP11-736I24.5" "PLXNC1"

## [1] 9
##  [1] "CALCR"                     "ZNF532"                   
##  [3] "MBNL3"                     "OPHN1"                    
##  [5] "MS4A4A"                    "ADGRG6"                   
##  [7] "LDAH"                      "MTERF1"                   
##  [9] "PIGC"                      "LRIG1"                    
## [11] "PSTPIP2"                   "PID1"                     
## [13] "RAB28"                     "PUS10"                    
## [15] "TMEM144"                   "DNAJC24"                  
## [17] "WDR25"                     "SDHAF3"                   
## [19] "PRDX6-AS1"                 "MAMDC2-AS1"               
## [21] "ZNF433-AS1"                "LINC00630"                
## [23] "RPL34-DT"                  "LINC01278"                
## [25] "RP11-195C7.1"              "LINC02432"                
## [27] "PVT1"                      "RP11-130F10.1"            
## [29] "LIX1-AS1"                  "LINC01605_ENSG00000253161"
## [31] "LINC01146"                 "DISC1FP1"                 
## [33] "EIF1B-AS1"                 "RP11-323F24.5"            
## [35] "RP4-545L17.11"             "PARP8"                    
## [37] "IL15"                      "TMEM65"                   
## [39] "APLF"                      "KCNE1"                    
## [41] "ZNF407"

## [1] 10
##  [1] "TPD52"      "RPL3"       "RPL18A"     "RPL19"      "RPL34"     
##  [6] "RPL24"      "ATP5F1E"    "FGF13"      "RPS24"      "PRDM5"     
## [11] "RPS2"       "RPS11"      "RPL11"      "SPAG16"     "RPL32"     
## [16] "FAU"        "BEND6"      "ATG10"      "RPL26"      "ELAVL4"    
## [21] "MRPL1"      "RPL38"      "RPLP2"      "RPS23"      "SPATS2L"   
## [26] "CPNE4"      "RPL12"      "RPL23A"     "RPL39"      "AIF1"      
## [31] "DOK6"       "SPOCK2"     "SLC1A2"     "ZMAT4"      "LPL"       
## [36] "ADARB1"     "LILRB3"     "SLC5A4-AS1"

## [1] 11
##  [1] "DERA"      "SNX24"     "ITGA6"     "POLA1"     "MID1"      "SUSD1"    
##  [7] "APBA1"     "MAP2K6"    "WLS"       "AKAP7"     "SLC10A7"   "DTD1"     
## [13] "METTL25"   "LANCL2"    "DPH6"      "NPL"       "IRF8"      "MMS22L"   
## [19] "NUBPL"     "SAMSN1"    "BACH1"     "C1QC"      "TNFRSF13C" "FILIP1L"  
## [25] "SLC35G2"   "C1QA"      "PTPN2"     "RTTN"      "PROS1"     "CCDC7"    
## [31] "HGF"       "FDFT1"     "HACE1"     "KLHL24"    "COL5A1"    "FNBP1L"   
## [37] "GOLIM4"

## [1] 12
##  [1] "NEXMIF"        "NAV3"          "CASS4"         "PLCL1"        
##  [5] "GARNL3"        "GIPC2"         "UNC80"         "TSPAN7"       
##  [9] "CACNA1D"       "RNF180"        "CCDC171"       "NAV2"         
## [13] "ZNF608"        "MACROD2"       "KCNIP1"        "ERC2"         
## [17] "COL25A1"       "ALOX12-AS1"    "LINC00539"     "RP11-535M15.1"
## [21] "STX18-AS1"     "LINC02232"     "MRPS30-DT"     "RP4-809F18.1" 
## [25] "RP11-370I10.6" "RP11-622O11.6" "COPG2IT1"      "RP11-640F22.1"
## [29] "RP11-320L2.1"  "DOCK3"         "CUX2"          "WDR45B"       
## [33] "KCND3"         "DPP10"         "ANKS1B"        "KCNIP4"       
## [37] "AIDA"          "RYR2"          "SNHG14"

## [1] 13
##  [1] "MCF2L2"   "CYFIP2"   "CST3"     "STS"      "ABCC4"    "DOCK10"  
##  [7] "BCAS3"    "FOXO1"    "BTG2"     "ANO10"    "ARHGAP25" "B2M"     
## [13] "BTD"      "SERPINB9" "XKR6"     "DYNC2H1"  "RPL41"    "RORA"    
## [19] "SLC1A3"   "DOCK9"    "PRKAG2"   "RAPGEF1"  "PTPRE"    "SSH2"    
## [25] "SDK1"     "MGAT5"    "FMNL2"    "RUNX1"    "CLASP2"   "OXR1"    
## [31] "LDLRAD4"  "GPHN"     "CEBPB"    "CHD2"     "BAIAP2"   "MYO1D"   
## [37] "PCDH9"    "GDI1"     "NEAT1"

## [1] 14
##  [1] "TNFRSF21" "JARID2"   "ARAP2"    "CPSF1"    "GRAMD4"   "PPP1R15A"
##  [7] "CEP170B"  "TBL1X"    "INTS6"    "HSF4"     "UBE2R2"   "DNAJC12" 
## [13] "DCUN1D4"  "BBX"      "CYTIP"    "TSHZ3"    "MGAT1"    "PHF21A"  
## [19] "IQGAP2"   "GFOD1"    "GNA12"    "THRB"     "RPP38"    "CAMK4"   
## [25] "RASSF3"   "ASAP1"    "RASA2"    "CDC42SE2" "SLMAP"    "STXBP5"  
## [31] "PCDH7"    "SH3PXD2B" "CMSS1"    "ARL4C"    "RALGAPA2" "IARS1"   
## [37] "ZNF277"   "EFCAB2"   "ZSCAN31"

## [1] 15
##  [1] "LRRC74A"    "MEIS1"      "ZNF707"     "HECW1"      "PKD1"      
##  [6] "NCDN"       "PTPRN"      "ITPKC"      "PCSK5"      "FLT1"      
## [11] "EPHA4"      "KDM5B"      "NR4A3"      "ZC4H2"      "AFDN"      
## [16] "EMILIN2"    "RAMP1"      "MACROD1"    "MICAL2"     "KCNK1"     
## [21] "CRIM1"      "NPAS3"      "CACNA2D1"   "PTPRN2"     "SORCS3"    
## [26] "PALM2AKAP2" "FGF17"      "SPTBN4"     "UNC5C"      "TSHZ2"     
## [31] "NELL2"      "ZBTB7C"     "PBX1"       "MIB2"       "SLC48A1"   
## [36] "MTRNR2L1"   "GRIN2B"

## [1] 16
##  [1] "PRKCQ"      "FOXP2"      "ATF5"       "XIST"       "GCLC"      
##  [6] "GCLM"       "PRKCH"      "WWC3"       "ZFAT"       "MYO9A"     
## [11] "ARHGAP15"   "ANKRD12"    "ADAP1"      "MEGF9"      "FOXP1"     
## [16] "SEM1"       "KIAA0513"   "CAMKMT"     "FER"        "RASGRP3"   
## [21] "MERTK"      "JAZF1"      "ADK"        "ST3GAL2"    "EPB41"     
## [26] "FBXO27"     "NEK10"      "MTSS1"      "MALT1"      "FUT10"     
## [31] "RESF1"      "SLC35E3"    "SAMD12"     "CSMD1"      "MAML2"     
## [36] "NPIPB15"    "CARD11"     "SOGA3"      "AC092835.2"

## [1] 17
##  [1] "ADGRD1"        "PDE10A"        "NEURL2"        "BANK1"        
##  [5] "ADAMTS3"       "UCN"           "PGBD5"         "TMEM151B"     
##  [9] "HDAC4-AS1"     "RP11-445F6.2"  "SMCR5"         "LINC01515"    
## [13] "LINC01277"     "RP3-525N10.2"  "LINC00271"     "LINC02884"    
## [17] "AC007682.1"    "RP11-142A5.1"  "AC073115.6"    "BDNF-AS"      
## [21] "LINC02211"     "RP11-115J16.1" "C5orf17"       "RP11-673E1.1" 
## [25] "LINC02055"     "FAM66D"        "MIR100HG"      "PRANCR"       
## [29] "CTD-2336H13.2" "LINC02073"     "CCDC28A-AS1"   "RP11-413N10.3"
## [33] "CERNA2"        "RP11-221G19.1" "LINC02885"     "RP11-237N2.1" 
## [37] "RP11-38B6.1"   "RP13-52K8.2"

## [1] 18
##  [1] "OSBPL5"                  "SNCAIP"                 
##  [3] "MGLL"                    "RPH3A"                  
##  [5] "GDAP1"                   "CD69"                   
##  [7] "PDE4D"                   "ZRANB3"                 
##  [9] "CHN1"                    "CALY"                   
## [11] "EFCAB11"                 "RNF157"                 
## [13] "NRGN"                    "ABCA5"                  
## [15] "CPLX1"                   "KCNMB2"                 
## [17] "ALG1L9P_ENSG00000248671" "CEROX1"                 
## [19] "ADAM22"                  "VCAN"                   
## [21] "PDE4A"                   "KCNAB2"                 
## [23] "RAB27A"                  "ZNF586"                 
## [25] "NCS1"                    "SASH1"                  
## [27] "HPCAL1"                  "SH3BP5"                 
## [29] "SNAP25"                  "PAM"                    
## [31] "MSI2"                    "STARD9"                 
## [33] "KALRN"                   "MSRA"                   
## [35] "CADM1"                   "PDE4B"                  
## [37] "KAZN"                    "UNC13B"                 
## [39] "MICAL3"

## [1] 19
##  [1] "ETV1"      "SCMH1"     "IGF1"      "PER3"      "APBB1IP"   "IL1A"     
##  [7] "IL1B"      "IL6ST"     "SLC22A23"  "TRPC1"     "MLIP"      "COPG2"    
## [13] "NLRP3"     "KIF26B"    "SFMBT1"    "TMEM52B"   "DTWD2"     "DENND5B"  
## [19] "DLEU1"     "SLC8A1"    "PRKN"      "SFMBT2"    "MBD5"      "LTC4S"    
## [25] "LIPE-AS1"  "MIR99AHG"  "MATK"      "RNASET2"   "RBFOX1"    "PDGFB"    
## [31] "LIFR"      "HPCAL4"    "SLC6A8"    "SLC2A5"    "FAT3"      "RBFOX3"   
## [37] "TNFRSF10C" "PCGF5"

## [1] 20
##  [1] "ZFP64"         "EFR3B"         "EPDR1"         "TXNDC16"      
##  [5] "PARD3B"        "GALNT12"       "IFT43"         "SIRPD"        
##  [9] "FBN2"          "TEX9"          "LINC00467"     "DISP1"        
## [13] "CLIC2"         "MAP3K7CL"      "AIM2"          "ATF7IP2"      
## [17] "TMC7"          "SPTLC3"        "RAB39A"        "FSIP2"        
## [21] "LEKR1"         "LINC01356"     "AC097721.2"    "RP5-1198O20.4"
## [25] "FSIP2-AS1"     "RP11-634B7.4"  "CDKN2B-AS1"    "LINC00968"    
## [29] "STARD4-AS1"    "RP11-120A1.1"  "RP11-10H3.1"   "MIR3142HG"    
## [33] "RHOXF1-AS1"    "LINC02666"     "RP1-111C20.3"  "GALNT18"      
## [37] "ARHGEF25"      "CPEB2-DT"      "CTB-41I6.2"

## [1] 21
##  [1] "ERCC8"   "OXCT1"   "ALDOC"   "CCDC18"  "DSTN"    "PIGK"    "IER2"   
##  [8] "BACE2"   "ABAT"    "CDK14"   "CDK17"   "TGFBR3"  "PGM1"    "NPDC1"  
## [15] "TPI1"    "SOD2"    "PAPOLG"  "HSPH1"   "CAMK1"   "DNAJB2"  "UACA"   
## [22] "CPNE8"   "MSN"     "MCPH1"   "CFDP1"   "PTMS"    "PCNT"    "GLRX"   
## [29] "AGFG1"   "FAM20C"  "ZDHHC20" "LIMK2"   "COL27A1" "HSPA1B"  "PPME1"

## [1] 22
##  [1] "ACKR4"         "HIVEP2"        "MAMLD1"        "HDHD5"        
##  [5] "MAP3K20"       "GADD45B"       "IL4I1"         "LILRB5"       
##  [9] "HS3ST2"        "TREM1"         "GPNMB"         "NIBAN2"       
## [13] "RASGEF1B"      "TAMALIN"       "IER5"          "ATOH8"        
## [17] "VMO1"          "ADSS1"         "ANKRD37"       "ZNF395"       
## [21] "TPRG1"         "H2BU1"         "AF064858.6"    "AS3MT"        
## [25] "FAM229A"       "LIMD1-AS1"     "DIRC3"         "DARS1-AS1"    
## [29] "RP11-47I22.3"  "AC009505.4"    "MIR155HG"      "AF064858.8"   
## [33] "SELENOP"       "LINC02698"     "CLEC5A"        "SAP30-DT"     
## [37] "MYOCOS"        "RP11-475M20.2" "CTD-2285E13.1" "RENO1"        
## [41] "RP11-134L10.2"

## [1] 23
##  [1] "RIPOR2"        "LILRB2"        "MCTP2"         "ABCA8"        
##  [5] "MTHFD2L"       "RAB37"         "ARSJ"          "CARNMT1-AS1"  
##  [9] "PCDH9-AS2"     "AC073115.7"    "TRG-AS1"       "RP11-341N18.1"
## [13] "RP11-120L14.1" "GALNT16"       "CDH20"         "MYOM1"        
## [17] "KATNAL1"       "STN1"          "ARFGEF3"       "ADAM23"       
## [21] "MXI1"          "ATP8A1"        "PCSK2"         "PATJ"         
## [25] "BTBD11"        "PITPNC1"       "FBXO32"        "ZFYVE28"      
## [29] "JAML"          "PLPP3"         "SNED1"         "AMER2"        
## [33] "KLF13"         "TBC1D10C"      "JAKMIP2"       "ZHX2"         
## [37] "TMTC2"         "SSTR2"         "CD247"         "CCDC71L"      
## [41] "LINC01138"

## [1] 24
##  [1] "RASGRP2"                 "FAM50A"                 
##  [3] "ADGRL1"                  "SLC26A3"                
##  [5] "AK1"                     "DRAM1"                  
##  [7] "CCNG2"                   "PGGHG"                  
##  [9] "PXDNL"                   "LRRC4C"                 
## [11] "CLEC1A"                  "AMN1"                   
## [13] "CFAP161"                 "TNFRSF11B"              
## [15] "SEMA3E"                  "LPCAT4"                 
## [17] "LINC00910"               "LINC00862"              
## [19] "LINC02397"               "C17orf67"               
## [21] "LINC01320"               "ARL17B"                 
## [23] "KLF3-AS1"                "SGO1-AS1"               
## [25] "AC067959.1"              "LINC01762"              
## [27] "RP3-467L1.4"             "LINC02646"              
## [29] "RP11-305L7.3"            "RP11-657O9.1"           
## [31] "LINC01322"               "RP11-17A1.3"            
## [33] "RP11-79E3.2"             "RP11-81K2.1"            
## [35] "SCARNA2_ENSG00000270066" "RP11-154H23.4"          
## [37] "RP11-114N19.3"           "RP11-344F5.1"           
## [39] "AC003099.2"

## [1] 25
##  [1] "MPP2"     "IRAK1BP1" "SKA2"     "CNTN1"    "LRRC7"    "CTNNA2"  
##  [7] "ZFY"      "ARHGAP10" "RAPGEF4"  "CELF4"    "KCNT1"    "CPE"     
## [13] "MOB3B"    "OLFM1"    "PDZD2"    "KCNH1"    "CDH18"    "CNKSR2"  
## [19] "ME3"      "SCN3A"    "FMN2"     "SYN2"     "EDIL3"    "NLGN1"   
## [25] "CTNND2"   "DLGAP1"   "C11orf80" "CNTNAP2"  "PPM1E"    "RIMS2"   
## [31] "NRXN1"    "OPCML"    "RALYL"    "OSBP2"    "PRKG1"    "SYN3"    
## [37] "MYT1L"    "MAGI2"    "GRM7"

## [1] 26
##  [1] "ADAM28"  "PROCR"   "NEK11"   "CCDC170" "SMAD6"   "MED12L"  "SAMD4A" 
##  [8] "NSMAF"   "LIMCH1"  "PHLPP1"  "IRAK3"   "FKBP5"   "USP9Y"   "FOXO3"  
## [15] "ELL2"    "RUNX2"   "DOCK6"   "ZNF331"  "IRAK2"   "CCNH"    "NHSL1"  
## [22] "FAM117B" "FAM13A"  "PELI2"   "MAP3K6"  "USP53"   "NEK7"    "PDE3B"  
## [29] "OTUD1"   "LRP1B"   "PPIP5K1" "BNC2"    "H2AC6"   "GPRIN3"  "SULF2"  
## [36] "PELI1"   "CEBPD"

## [1] 27
##  [1] "IPCEF1"     "PEX7"       "ITPR2"      "C3"         "STAMBPL1"  
##  [6] "GSTCD"      "FRMD6"      "ITGA9"      "TBC1D32"    "FRMD4A"    
## [11] "LRRC8C"     "ZMAT3"      "ATAD5"      "CA8"        "SLC9A9"    
## [16] "CACNB4"     "MEI4"       "SCIN"       "CLEC16A"    "LCP2"      
## [21] "PAG1"       "CTTNBP2"    "RFX3"       "RFX2"       "RASSF8"    
## [26] "ARHGAP22"   "PRAM1"      "WNT2B"      "GYPC"       "CSGALNACT1"
## [31] "DIXDC1"     "SH3RF1"     "DHRSX"      "PACS1"      "FADS3"

## [1] 28
##  [1] "PKD2L2"         "IL7"            "SGCE"           "MIR4435-2HG"   
##  [5] "GLIPR1L1"       "TTTY14"         "MCMDC2"         "EYS"           
##  [9] "RP1-225E12.2"   "RP5-1132H15.1"  "LANCL1-AS1"     "ITGA9-AS1"     
## [13] "RMDN2-AS1"      "LRIG2-DT"       "RP11-775D22.3"  "RP11-544A12.8" 
## [17] "RP11-506H20.1"  "RP11-1H15.2"    "RP11-867G2.8"   "RP11-571M6.7"  
## [21] "RP11-160E2.6"   "RP11-703M24.5"  "CEACAM16-AS1"   "KCNQ1OT1"      
## [25] "RP11-74J13.8"   "RP11-305E17.8"  "RP11-793H13.14" "RP1-18C9.3"    
## [29] "RP11-65F13.4"   "RP11-13J12.3"   "RP11-6G22.1"    "RP11-685G9.5"  
## [33] "RP11-555K12.4"  "RP11-617F9.2"   "ST3GAL1"        "SLC9A7"        
## [37] "PCDH11Y"        "APBB3"          "H1-10"          "RP11-37N22.1"  
## [41] "RP11-384C4.7"   "RP11-322M13.1"

## [1] 29
##  [1] "PLPP1"         "ACER3"         "SP140"         "CARMIL1"      
##  [5] "ZNF821"        "RCAN3"         "PLAGL1"        "SSPN"         
##  [9] "PUDP"          "SPATA6"        "TBC1D14"       "EPHB2"        
## [13] "ARHGAP20"      "SLC49A4"       "NKD1"          "WDPCP"        
## [17] "C11orf49"      "CD226"         "DENND2B"       "FGGY"         
## [21] "B3GNT5"        "PCED1B"        "SCFD2"         "FIRRE"        
## [25] "LINC02649"     "FTCDNL1"       "RP11-162D16.2" "RP11-202G18.1"
## [29] "RFX3-AS1"      "RP11-557H15.4" "LINC00884"     "LINC01184"    
## [33] "LINC02762"     "LINC02328"     "RP11-154H12.3" "TSIX"         
## [37] "RP11-323P17.2" "MIR223HG"      "RP11-419I17.1" "SEC14L1"

## [1] 30
##  [1] "HTR2B"        "TAGAP"        "PNMA3"        "TWIST2"       "NFIX"        
##  [6] "TNS1"         "RNF24"        "RNMT"         "BNIP3L"       "GYS1"        
## [11] "ARRDC2"       "GBE1"         "RLF"          "SPP1"         "IQSEC2"      
## [16] "SOX5"         "IQSEC1"       "SLC25A37"     "RIT2"         "AGPAT5"      
## [21] "MAPK13"       "SSBP3"        "ETS2"         "ABCG1"        "ABCA1"       
## [26] "DDIT4"        "SNTB2"        "CRADD"        "PPP1R3B"      "BNIP3"       
## [31] "FAM210A"      "CHST15"       "H1-0"         "RGL3"         "AC093818.1"  
## [36] "RP11-13N12.1" "FMNL1-DT"

## [1] 31
##  [1] "PDK4"          "NLRP1"         "CPED1"         "PEBP4"        
##  [5] "GPAT3"         "CFAP74"        "GASK1A"        "TENM4"        
##  [9] "SETBP1"        "C4orf19"       "DEPTOR"        "MIR31HG"      
## [13] "CYSLTR1"       "KCNQ3"         "RTN4RL1"       "CLEC9A"       
## [17] "LINC01285"     "RP11-131L23.1" "LINC01357"     "AC105760.2"   
## [21] "KIF9-AS1"      "HDAC2-AS2"     "HMGA1P4"       "MIR4300HG"    
## [25] "CTB-161M19.4"  "ZFPM2-AS1"     "LINC01301"     "RP11-946L16.1"
## [29] "RP11-187O7.3"  "MRC1"          "ATP6V0D1-DT"   "RP11-495L19.1"
## [33] "RP11-437L7.2"  "RP11-168F24.3" "RP11-4F5.3"    "KCNQ2"        
## [37] "HTR1E"         "KCNQ5"         "RP11-249L21.6"

## [1] 32
##  [1] "TTC7A"                   "NIPAL2"                 
##  [3] "GAREM1"                  "SESN3"                  
##  [5] "PLXDC1"                  "HESX1"                  
##  [7] "NMNAT3"                  "LIPC"                   
##  [9] "PLD4"                    "CX3CR1"                 
## [11] "ACYP2"                   "ZDHHC14"                
## [13] "CATSPERE"                "SPATA13_ENSG00000182957"
## [15] "RNLS"                    "B3GLCT"                 
## [17] "AC003090.1"              "ENTPD3-AS1"             
## [19] "TMEM72-AS1"              "CTA-292E10.6"           
## [21] "TEX41"                   "LMCD1-AS1"              
## [23] "RP13-188A5.1"            "MIR646HG"               
## [25] "HCG22"                   "ZRANB2-AS2"             
## [27] "LINC01376"               "RNF217-AS1"             
## [29] "MEF2C-AS1"               "RP11-319G6.1"           
## [31] "RP11-381K20.2"           "RP11-692D12.1"          
## [33] "GMDS-DT"                 "RP11-679C8.2"           
## [35] "C8orf37-AS1"             "RP11-541P9.3"           
## [37] "RP11-511B23.2"           "LINC00907"              
## [39] "MIR222HG"                "RP11-111G13.1"          
## [41] "RP11-685G11.1"

## [1] 33
##  [1] "MUSK"         "ANGPT2"       "ECM2"         "FMO5"         "BCL2A1"      
##  [6] "ZDHHC19"      "BEAN1"        "GLYATL1"      "MOBP"         "RP11-621L6.2"
## [11] "SLC2A3"       "ABCA7"        "PLEKHH3"      "ANO8"         "RAP1GAP"     
## [16] "HIF3A"        "CHI3L1"       "BTG1"         "CEMIP2"       "HILPDA"      
## [21] "ADCY3"        "RGS16"        "TMEM140"      "ST18"         "PLIN2"       
## [26] "LYPD5"        "CCDC107"      "ANKZF1"       "NFIL3"        "ALDH1A1"     
## [31] "ADCY5"        "RBM44"        "CD55"         "ERO1A"        "SH3BGRL2"    
## [36] "STARD10"      "SLC12A8"      "HIF1A-AS3"

## [1] 34
##  [1] "ATP8B1"        "SLC5A9"        "SHOC1"         "ENO4"         
##  [5] "INSYN2B"       "ANKUB1"        "AC002463.3"    "ELMO1-AS1"    
##  [9] "TMLHE-AS1"     "AC096558.1"    "RP4-568F9.6"   "AC083884.8"   
## [13] "AC037445.1"    "CPB2-AS1"      "MYCBP2-AS1"    "DIAPH2-AS1"   
## [17] "CCDC200"       "AC018890.6"    "LINC01877"     "MEF2C-AS2"    
## [21] "CTD-2015H6.3"  "RHOQ-AS1"      "RP11-268P4.5"  "AP000487.6"   
## [25] "RP11-638I2.8"  "LINC02316"     "USP3-AS1"      "RP11-815J21.4"
## [29] "RP11-16B9.1"   "PRKCA-AS1"     "RP11-16C1.3"   "RP11-793A3.2" 
## [33] "RP11-58G13.1"  "RP1-256G22.2"  "CTD-2282P23.2" "DISC2"        
## [37] "RP11-314L11.1" "RP11-261A24.1" "RP11-1H15.4"   "RP11-1146N6.3"
## [41] "SLC26A7"

## [1] 35
##  [1] "HHAT"         "XAF1"         "FBXL13"       "PAQR3"        "LINC00624"   
##  [6] "MSR1"         "PDE8A"        "RGS1"         "DARS1"        "GTDC1"       
## [11] "SRGN"         "RGL1"         "MYO10"        "TNFAIP8"      "ARHGAP18"    
## [16] "RSU1"         "HTR7"         "ARID5B"       "NGLY1"        "ACSL1"       
## [21] "FRRS1"        "ACOT11"       "CDCP1"        "RHOBTB3"      "MARCHF8"     
## [26] "ALCAM"        "KLHL6"        "MFSD4B"       "TNFAIP8L3"    "MITF"        
## [31] "DPYD"         "PARVB"        "CTD-3088G3.8" "UBXN2B"       "PIK3IP1-DT"  
## [36] "MIR181A1HG"   "CTD-2643I7.5" "IFITM10"      "SBF2-AS1"

## [1] 36
##  [1] "CRYM"          "IGSF11"        "GLT1D1"        "TSBP1-AS1"    
##  [5] "KIF5C-AS1"     "MEIKIN"        "MTRNR2L8"      "PSMD7-DT"     
##  [9] "SYT7"          "COL5A3"        "IGSF9B"        "NALCN"        
## [13] "DNAH6"         "CHD5"          "CSMD2"         "CBLN2"        
## [17] "CFAP251"       "PDZRN4"        "STXBP6"        "CXXC5"        
## [21] "CADM2"         "SRRM3"         "ADGRB1"        "NRG3"         
## [25] "SLIT1"         "CR1L"          "RORB"          "FAM153CP"     
## [29] "BASP1-AS1"     "MIAT"          "TRHDE-AS1"     "RP11-259O2.1" 
## [33] "LINC01414"     "CTC-535M15.2"  "RP11-429A20.3" "RP11-368L12.1"
## [37] "LINC00558"     "U91319.1"      "RP11-436D23.1" "RP5-1015P16.1"
## [41] "RP11-335E8.3"

## [1] 37
##  [1] "ICA1"          "PRDM11"        "ST6GAL1"       "SLC26A4"      
##  [5] "PODXL2"        "AOPEP"         "LY96"          "SMIM14"       
##  [9] "PRMT9"         "GPR34"         "GAP43"         "CAPS2"        
## [13] "CDIN1"         "SRGAP3"        "CHSY3"         "C12orf75"     
## [17] "LINC00894"     "LINC01684"     "RP11-37B2.1"   "RP11-630C16.2"
## [21] "RP11-574F11.4" "STAB1"         "SESN1"         "TMED8"        
## [25] "IL27RA"        "NCOA7"         "FRMD4B"        "TMEM115"      
## [29] "CHSY1"         "SLC41A2"       "TLR2"          "DHRS3"        
## [33] "ROBO1"         "RNF150"        "LONRF3"        "TRNAU1AP"     
## [37] "TLR5"          "ZC3H6"

## [1] 38
##  [1] "CECR2"       "NME3"        "ABCC1"       "OGN"         "PLGRKT"     
##  [6] "IFIT3"       "IFIT2"       "CENPK"       "SAT1"        "RTN4IP1"    
## [11] "PCBD2"       "ITM2C"       "ERMN"        "TET1"        "LPAR6"      
## [16] "PTH2R"       "ADGRG5"      "FAM227B"     "RIC3"        "TLN2"       
## [21] "NAALADL2"    "ZFP36L1"     "IFIT1"       "DNAH14"      "ZNRF1"      
## [26] "CH17-55D9.1" "RP6-91H8.6"  "RP4-681L3.3" "ATP9A"       "RGCC"       
## [31] "TGFBI"       "ATP8B2"      "KIF5C"       "KLC2"        "MAMDC4"     
## [36] "IFNLR1"      "GK"

## [1] 39
##  [1] "PLEK"          "CYREN"         "RAB38"         "MMP24"        
##  [5] "OMD"           "TMEM241"       "IER3"          "AGBL3"        
##  [9] "NLGN4Y"        "CYTL1"         "IRAG1-AS1"     "H2AC20"       
## [13] "AC023590.1"    "ARHGAP26-AS1"  "ZNF451-AS1"    "AC105461.1"   
## [17] "ALG13-AS1"     "ARHGAP15-AS1"  "IPO9-AS1"      "RAP2C-AS1"    
## [21] "UFL1-AS1"      "RP11-528G1.2"  "FBXO30-DT"     "KDM4A-AS1"    
## [25] "BCL2L1-AS1"    "RP11-544A12.4" "DENND6A-AS1"   "ZBTB20-AS5"   
## [29] "GPRC5D-AS1"    "RP11-434H14.1" "LINC00639"     "RP11-106M3.3" 
## [33] "RNF213-AS1"    "H2BC7"         "RP11-121C2.3"  "RP11-19D22.1" 
## [37] "RP11-622I12.1" "RP11-458A7.1"  "RP11-21M24.6"  "RP11-314E10.1"
## [41] "RP11-399K19.1"

## [1] 40
##  [1] "ANGPTL1"       "C11orf65"      "COL5A2"        "SPDYE2"       
##  [5] "MTCP1"         "RP11-321C24.1" "DOCK4-AS1"     "RP11-165F24.3"
##  [9] "AC017101.10"   "RP11-526K17.2" "RP11-575L7.8"  "RP1-117O3.2"  
## [13] "KCNMA1-AS1"    "LINC00960"     "RP11-712B9.2"  "ANK2-AS1"     
## [17] "CTD-2227I18.1" "LINC02742"     "RP11-39E3.3"   "CTD-3239E11.2"
## [21] "RP11-624C23.1" "RP11-463D19.1" "CTD-2537O9.1"  "RP11-493L12.3"
## [25] "RP11-713N11.4" "CTD-2647E9.3"  "RP11-317G6.1"  "RP11-516C1.1" 
## [29] "LMO7-AS1"      "RP11-66H6.3"   "LINC00621"     "RP11-737O24.2"
## [33] "TCF4-AS1"      "RP11-53B2.3"   "RP11-126O1.4"  "CTD-3149D2.4" 
## [37] "RP4-769N13.7"  "H2AC19"        "RP11-275G7.2"  "GS1-98E2.1"   
## [41] "RP1-80B9.4"    "CTD-2021K4.2"

for(n1 in names(goseq_res)){
  k = as.numeric(gsub("set_", "", n1))
  print(n1)
  print(gene_sets[[k]])
  print(goseq_res[[n1]])

}
## [1] "set_8"
##  [1] "SIGLEC1"       "PCSK1N"        "MAP3K8"        "FLVCR2"       
##  [5] "F13A1"         "ENOSF1"        "IFI44L"        "CH25H"        
##  [9] "HERC6"         "UBE2Q2"        "FHAD1"         "TMEM44"       
## [13] "ADAMTS19"      "ADGRA3"        "BEX3"          "MT1E"         
## [17] "OLR1"          "ODF3B"         "H2BC4"         "MX2"          
## [21] "H2BC18"        "TMSB4X"        "MS4A4E"        "RP11-123B3.2" 
## [25] "RP5-1101C3.1"  "ARHGAP8"       "LINC01258"     "LINC02196"    
## [29] "ZNF10"         "RP1-71H24.1"   "OVCH1-AS1"     "RP11-323I15.5"
## [33] "LINC01572"     "RP11-386I14.4" "H2BC8"         "H2AC8"        
## [37] "RP11-736I24.5" "PLXNC1"       
## $reactome
##                       category over_represented_pvalue under_represented_pvalue
## 412    hats acetylate histones            4.170912e-05                0.9999991
## 415           hcmv late events            6.723915e-05                0.9999982
## 416 hdacs deacetylate histones            7.108510e-05                0.9999981
##     numDEInCat numInCat        FDR
## 412          4        9 0.02800753
## 415          4       11 0.02800753
## 416          4       11 0.02800753
## 
## [1] "set_10"
##  [1] "TPD52"      "RPL3"       "RPL18A"     "RPL19"      "RPL34"     
##  [6] "RPL24"      "ATP5F1E"    "FGF13"      "RPS24"      "PRDM5"     
## [11] "RPS2"       "RPS11"      "RPL11"      "SPAG16"     "RPL32"     
## [16] "FAU"        "BEND6"      "ATG10"      "RPL26"      "ELAVL4"    
## [21] "MRPL1"      "RPL38"      "RPLP2"      "RPS23"      "SPATS2L"   
## [26] "CPNE4"      "RPL12"      "RPL23A"     "RPL39"      "AIF1"      
## [31] "DOK6"       "SPOCK2"     "SLC1A2"     "ZMAT4"      "LPL"       
## [36] "ADARB1"     "LILRB3"     "SLC5A4-AS1"
## $reactome
##                                              category over_represented_pvalue
## 138                   cellular response to starvation                       0
## 301                 eukaryotic translation elongation                       0
## 302                 eukaryotic translation initiation                       0
## 452                               influenza infection                       0
## 557         metabolism of amino acids and derivatives                       0
## 640                       nonsense mediated decay nmd                       0
## 801       regulation of expression of slits and robos                       0
## 850 response of eif2ak4 gcn2 to amino acid deficiency                       0
## 901                                   rrna processing                       0
## 927                       selenoamino acid metabolism                       0
##     under_represented_pvalue numDEInCat numInCat FDR
## 138                        1         18       26   0
## 301                        1         18       23   0
## 302                        1         18       23   0
## 452                        1         18       27   0
## 557                        1         18       41   0
## 640                        1         18       23   0
## 801                        1         18       27   0
## 850                        1         18       25   0
## 901                        1         18       25   0
## 927                        1         18       26   0
## 
## $go_bp
##                                category over_represented_pvalue
## 630             cytoplasmic translation            0.000000e+00
## 4283                ribosome biogenesis            2.296868e-10
## 4279 ribosomal large subunit biogenesis            1.498704e-08
## 4278   ribosomal large subunit assembly            5.811626e-07
## 4281 ribosomal small subunit biogenesis            2.783323e-06
## 4282                  ribosome assembly            2.822337e-06
##      under_represented_pvalue numDEInCat numInCat          FDR
## 630                         1         18       23 0.000000e+00
## 4283                        1          8       13 5.420610e-07
## 4279                        1          5        5 2.357960e-05
## 4278                        1          4        4 6.857719e-04
## 4281                        1          4        5 2.220238e-03
## 4282                        1          4        5 2.220238e-03
## 
## [1] "set_12"
##  [1] "NEXMIF"        "NAV3"          "CASS4"         "PLCL1"        
##  [5] "GARNL3"        "GIPC2"         "UNC80"         "TSPAN7"       
##  [9] "CACNA1D"       "RNF180"        "CCDC171"       "NAV2"         
## [13] "ZNF608"        "MACROD2"       "KCNIP1"        "ERC2"         
## [17] "COL25A1"       "ALOX12-AS1"    "LINC00539"     "RP11-535M15.1"
## [21] "STX18-AS1"     "LINC02232"     "MRPS30-DT"     "RP4-809F18.1" 
## [25] "RP11-370I10.6" "RP11-622O11.6" "COPG2IT1"      "RP11-640F22.1"
## [29] "RP11-320L2.1"  "DOCK3"         "CUX2"          "WDR45B"       
## [33] "KCND3"         "DPP10"         "ANKS1B"        "KCNIP4"       
## [37] "AIDA"          "RYR2"          "SNHG14"       
## $reactome
##               category over_represented_pvalue under_represented_pvalue
## 113 cardiac conduction            2.383914e-05                0.9999995
## 599 muscle contraction            5.461467e-05                0.9999986
##     numDEInCat numInCat        FDR
## 113          4       18 0.02817787
## 599          4       24 0.03227727
## 
## [1] "set_16"
##  [1] "PRKCQ"      "FOXP2"      "ATF5"       "XIST"       "GCLC"      
##  [6] "GCLM"       "PRKCH"      "WWC3"       "ZFAT"       "MYO9A"     
## [11] "ARHGAP15"   "ANKRD12"    "ADAP1"      "MEGF9"      "FOXP1"     
## [16] "SEM1"       "KIAA0513"   "CAMKMT"     "FER"        "RASGRP3"   
## [21] "MERTK"      "JAZF1"      "ADK"        "ST3GAL2"    "EPB41"     
## [26] "FBXO27"     "NEK10"      "MTSS1"      "MALT1"      "FUT10"     
## [31] "RESF1"      "SLC35E3"    "SAMD12"     "CSMD1"      "MAML2"     
## [36] "NPIPB15"    "CARD11"     "SOGA3"      "AC092835.2"
## $reactome
##                                                category over_represented_pvalue
## 314                     fceri mediated nf kb activation            1.618734e-05
## 391                             glutathione conjugation            1.308212e-04
## 392                 glutathione synthesis and recycling            1.308212e-04
## 555 metabolic disorders of biological oxidation enzymes            1.308212e-04
## 258  downstream signaling events of b cell receptor bcr            1.341146e-04
##     under_represented_pvalue numDEInCat numInCat        FDR
## 314                0.9999997          4        8 0.01913344
## 391                1.0000000          2        2 0.03170469
## 392                1.0000000          2        2 0.03170469
## 555                1.0000000          2        2 0.03170469
## 258                0.9999958          4       10 0.03170469
## 
## [1] "set_18"
##  [1] "OSBPL5"                  "SNCAIP"                 
##  [3] "MGLL"                    "RPH3A"                  
##  [5] "GDAP1"                   "CD69"                   
##  [7] "PDE4D"                   "ZRANB3"                 
##  [9] "CHN1"                    "CALY"                   
## [11] "EFCAB11"                 "RNF157"                 
## [13] "NRGN"                    "ABCA5"                  
## [15] "CPLX1"                   "KCNMB2"                 
## [17] "ALG1L9P_ENSG00000248671" "CEROX1"                 
## [19] "ADAM22"                  "VCAN"                   
## [21] "PDE4A"                   "KCNAB2"                 
## [23] "RAB27A"                  "ZNF586"                 
## [25] "NCS1"                    "SASH1"                  
## [27] "HPCAL1"                  "SH3BP5"                 
## [29] "SNAP25"                  "PAM"                    
## [31] "MSI2"                    "STARD9"                 
## [33] "KALRN"                   "MSRA"                   
## [35] "CADM1"                   "PDE4B"                  
## [37] "KAZN"                    "UNC13B"                 
## [39] "MICAL3"                 
## $reactome
##                                          category over_represented_pvalue
## 203                               darpp 32 events            0.0000162074
## 6    acetylcholine neurotransmitter release cycle            0.0001171809
## 641 norepinephrine neurotransmitter release cycle            0.0001171809
##     under_represented_pvalue numDEInCat numInCat        FDR
## 203                1.0000000          3        3 0.01915715
## 6                  0.9999988          3        5 0.04616926
## 641                0.9999988          3        5 0.04616926
## 
## [1] "set_19"
##  [1] "ETV1"      "SCMH1"     "IGF1"      "PER3"      "APBB1IP"   "IL1A"     
##  [7] "IL1B"      "IL6ST"     "SLC22A23"  "TRPC1"     "MLIP"      "COPG2"    
## [13] "NLRP3"     "KIF26B"    "SFMBT1"    "TMEM52B"   "DTWD2"     "DENND5B"  
## [19] "DLEU1"     "SLC8A1"    "PRKN"      "SFMBT2"    "MBD5"      "LTC4S"    
## [25] "LIPE-AS1"  "MIR99AHG"  "MATK"      "RNASET2"   "RBFOX1"    "PDGFB"    
## [31] "LIFR"      "HPCAL4"    "SLC6A8"    "SLC2A5"    "FAT3"      "RBFOX3"   
## [37] "TNFRSF10C" "PCGF5"    
## $go_bp
##                                             category over_represented_pvalue
## 2767 positive regulation of mitotic nuclear division            1.062274e-06
## 2818         positive regulation of nuclear division            1.062274e-06
## 3678          regulation of mitotic nuclear division            1.878468e-06
## 3750                  regulation of nuclear division            1.878468e-06
## 37                       acute inflammatory response            4.198804e-05
##      under_represented_pvalue numDEInCat numInCat         FDR
## 2767                1.0000000          4        7 0.002216593
## 2818                1.0000000          4        7 0.002216593
## 3678                1.0000000          4        8 0.002216593
## 3750                1.0000000          4        8 0.002216593
## 37                  0.9999991          4        8 0.039636712
## 
## [1] "set_26"
##  [1] "ADAM28"  "PROCR"   "NEK11"   "CCDC170" "SMAD6"   "MED12L"  "SAMD4A" 
##  [8] "NSMAF"   "LIMCH1"  "PHLPP1"  "IRAK3"   "FKBP5"   "USP9Y"   "FOXO3"  
## [15] "ELL2"    "RUNX2"   "DOCK6"   "ZNF331"  "IRAK2"   "CCNH"    "NHSL1"  
## [22] "FAM117B" "FAM13A"  "PELI2"   "MAP3K6"  "USP53"   "NEK7"    "PDE3B"  
## [29] "OTUD1"   "LRP1B"   "PPIP5K1" "BNC2"    "H2AC6"   "GPRIN3"  "SULF2"  
## [36] "PELI1"   "CEBPD"  
## $go_bp
##                    category over_represented_pvalue under_represented_pvalue
## 4565 toll signaling pathway            9.170054e-06                0.9999999
##      numDEInCat numInCat        FDR
## 4565          4        5 0.04328265
## 
## [1] "set_31"
##  [1] "PDK4"          "NLRP1"         "CPED1"         "PEBP4"        
##  [5] "GPAT3"         "CFAP74"        "GASK1A"        "TENM4"        
##  [9] "SETBP1"        "C4orf19"       "DEPTOR"        "MIR31HG"      
## [13] "CYSLTR1"       "KCNQ3"         "RTN4RL1"       "CLEC9A"       
## [17] "LINC01285"     "RP11-131L23.1" "LINC01357"     "AC105760.2"   
## [21] "KIF9-AS1"      "HDAC2-AS2"     "HMGA1P4"       "MIR4300HG"    
## [25] "CTB-161M19.4"  "ZFPM2-AS1"     "LINC01301"     "RP11-946L16.1"
## [29] "RP11-187O7.3"  "MRC1"          "ATP6V0D1-DT"   "RP11-495L19.1"
## [33] "RP11-437L7.2"  "RP11-168F24.3" "RP11-4F5.3"    "KCNQ2"        
## [37] "HTR1E"         "KCNQ5"         "RP11-249L21.6"
## $reactome
##                              category over_represented_pvalue
## 1177 voltage gated potassium channels            3.132597e-05
##      under_represented_pvalue numDEInCat numInCat       FDR
## 1177                0.9999998          3        7 0.0370273
saveRDS(goseq_res, sprintf("output/gene_set_enrichments_%s.RDS", 
                           file_tag))

Session information

gc()
##            used  (Mb) gc trigger  (Mb) limit (Mb) max used  (Mb)
## Ncells  8955084 478.3   16112782 860.6         NA 16112782 860.6
## Vcells 16667379 127.2   31295163 238.8      65536 31295163 238.8
sessionInfo()
## R version 4.2.3 (2023-03-15)
## Platform: aarch64-apple-darwin20 (64-bit)
## Running under: macOS Ventura 13.4.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] goseq_1.50.0           geneLenDataBase_1.34.0 BiasedUrn_2.0.10      
##  [4] fgsea_1.24.0           biomaRt_2.54.1         limma_3.54.2          
##  [7] tidyr_1.3.0            ggpubr_0.6.0           ggplot2_3.4.2         
## [10] data.table_1.14.8     
## 
## loaded via a namespace (and not attached):
##   [1] nlme_3.1-162                matrixStats_1.0.0          
##   [3] bitops_1.0-7                bit64_4.0.5                
##   [5] filelock_1.0.2              progress_1.2.2             
##   [7] httr_1.4.6                  GenomeInfoDb_1.34.9        
##   [9] tools_4.2.3                 backports_1.4.1            
##  [11] bslib_0.4.2                 utf8_1.2.3                 
##  [13] R6_2.5.1                    mgcv_1.8-42                
##  [15] DBI_1.1.3                   BiocGenerics_0.44.0        
##  [17] colorspace_2.1-0            withr_2.5.0                
##  [19] tidyselect_1.2.0            prettyunits_1.1.1          
##  [21] bit_4.0.5                   curl_5.0.1                 
##  [23] compiler_4.2.3              cli_3.6.1                  
##  [25] Biobase_2.58.0              xml2_1.3.4                 
##  [27] DelayedArray_0.24.0         rtracklayer_1.58.0         
##  [29] sass_0.4.5                  scales_1.2.1               
##  [31] rappdirs_0.3.3              Rsamtools_2.14.0           
##  [33] stringr_1.5.0               digest_0.6.31              
##  [35] rmarkdown_2.21              XVector_0.38.0             
##  [37] pkgconfig_2.0.3             htmltools_0.5.5            
##  [39] MatrixGenerics_1.10.0       dbplyr_2.3.2               
##  [41] fastmap_1.1.1               rlang_1.1.0                
##  [43] rstudioapi_0.14             RSQLite_2.3.1              
##  [45] BiocIO_1.8.0                jquerylib_0.1.4            
##  [47] generics_0.1.3              jsonlite_1.8.4             
##  [49] BiocParallel_1.32.6         dplyr_1.1.2                
##  [51] car_3.1-2                   RCurl_1.98-1.12            
##  [53] magrittr_2.0.3              GO.db_3.16.0               
##  [55] GenomeInfoDbData_1.2.9      Matrix_1.6-4               
##  [57] Rcpp_1.0.10                 munsell_0.5.0              
##  [59] S4Vectors_0.36.2            fansi_1.0.4                
##  [61] abind_1.4-5                 lifecycle_1.0.3            
##  [63] stringi_1.7.12              yaml_2.3.7                 
##  [65] carData_3.0-5               SummarizedExperiment_1.28.0
##  [67] zlibbioc_1.44.0             org.Hs.eg.db_3.16.0        
##  [69] BiocFileCache_2.6.1         grid_4.2.3                 
##  [71] blob_1.2.4                  parallel_4.2.3             
##  [73] crayon_1.5.2                lattice_0.20-45            
##  [75] splines_4.2.3               Biostrings_2.66.0          
##  [77] cowplot_1.1.1               GenomicFeatures_1.50.4     
##  [79] hms_1.1.3                   KEGGREST_1.38.0            
##  [81] knitr_1.44                  pillar_1.9.0               
##  [83] GenomicRanges_1.50.2        rjson_0.2.21               
##  [85] ggsignif_0.6.4              codetools_0.2-19           
##  [87] stats4_4.2.3                fastmatch_1.1-3            
##  [89] XML_3.99-0.14               glue_1.6.2                 
##  [91] evaluate_0.20               png_0.1-8                  
##  [93] vctrs_0.6.2                 gtable_0.3.3               
##  [95] purrr_1.0.1                 cachem_1.0.7               
##  [97] xfun_0.39                   broom_1.0.4                
##  [99] restfulr_0.0.15             rstatix_0.7.2              
## [101] tibble_3.2.1                GenomicAlignments_1.34.1   
## [103] AnnotationDbi_1.60.2        memoise_2.0.1              
## [105] IRanges_2.32.0